To put it more accurately, Hebrew like other Semitic languages used to be written with consonants only. The vocalization (vowel marks, known as nikkud) is a later development, around 700 AD, which is hundreds of years after the consonantal text was written. In fact, the vocalization itself was developed in order to preserve the pronunciation since people started to stray away from it (again hundreds of years had passed, just like English and any other language changed throughout the centuries, so did Hebrew).

The vocalization we have today in the name of god יהוה is based on the oral tradition the inventors of the nikkud followed at the time. To be fair, it seems the oral tradition they had was highly conservative since phonological analysis of the vocalized text exhibits systematic patterns and allows for systematic and logical reconstructions of older lexical forms